A group of asylum seekers who arrived in Geraldton, about 400 kilometres north of Perth, have undergone health and security checks and were waiting to be transferred to detention facilities late on Tuesday night.

Geraldton is 2,240 kilometres south of Christmas Island, the usual destination of asylum seekers heading for Australia.

It is understood two men in a dinghy first spotted the boat and alerted authorities just after midday (AWST) on Tuesday.

Authorities say the boat was undetected until it made it into the harbour.

The Immigration Department says it planned to send the male asylum seekers to a detention facility in Northam, 460 kilometres south-west of Geraldton, late Tuesday.

Women, children and family groups will be relocated to another facility away from Geraldton, however the department will not confirm where.

The Immigration Department says all 66 asylum seekers will then be transferred to Christmas Island.

However, lawyer David Manne from the Refugee and Immigration Legal Centre says the asylum seekers can avoid being sent offshore by applying for refugee status.

Mr Mann has told the ABC the group has different rights to other asylum seekers because they landed on the Australian mainland.

He says they are entitled to legal representation and may be able to avoid offshore detention.

"If they apply for refugee protection in Australia, under Australian due legal process, they're entitled to have their claims assessed here and to not be sent elsewhere," he said.

It is unclear how the boat made it so far south before being spotted.

Those on board were carrying a sign that says they want to go to New Zealand.

Home Affairs Minister Jason Clare released a statement saying Customs and Border Protection officers as well as Western Australian Police responded to the arrival.

'Serious breach'

WA Premier Colin Barnett has described the incident as a "serious, unprecedented and unacceptable breach of Australia's border security".

"It's a serious lapse and I simply cannot imagine how this could have occurred," he said.

"For a boat, in broad daylight, to have sailed onto the Australian mainland, in the south of the state and just blatantly sail into Geraldton, that is extraordinary.

"I think there needs to be some questions answered about that.

"I think the immediate issue though is to make sure people are well cared for, that there's no health risk or safety risk to the local community. I'm assured that's being handled well and is in control."